Those ferries should be switching the direction the crew faces (perhaps in a different structure on the other end of the boat) and turning on the appropriate lights so port and starboard are lit correctly. They should have two sets of colored lights to handle travel in both directions.
Don't they have to swap the lights anyway if the ferry reverses direction? After all, the red/green indicators are primarily for showing which direction the ship is moving in.
With double ended ferries you're going to dock bow first because that's the direction all the cars pointed.
If you got halfway through a crossing and they announced there's a problem at the destination (broken thruster, docks on fire, dragons, docks on fire because of dragons), you would have to turn the ship around 180º and go back to your origin with the same bow that you started the trip with so everyone could disembark. The only time you'd switch ship orientation mid-trip is if something broke such that one end of the ship was navigable and the other was not. At which point you'd either have to dock backward (maybe with a tug) or everyone would have to back off the ship.
